When the 49ers chased Peyton Manning–with Alex Smith and Colin Kaepernick on the roster–and what it means now

Yep, there’s little doubt that Jim Harbaugh, Trent Baalke, Jed York and Greg Roman can get very aggressive with personnel at the quarterback position.

Let’s flash back to March 2012, when the 49ers charged hard after free agent Peyton Manning, who had just been released by Indianapolis… while they also had a 3-year, $24M offer on the table to Alex Smith (their incumbent, playoff-game-winning starter) and had Colin Kaepernick, too.

So, in the wake of a very frustrating loss to the NY Giants in the NFC Championship Game, the 49ers were scheming and hoping for a theoretical QB depth chart of:

1-Manning, 2-Smith, 3-Kaepernick… (though they also knew Smith could and probably would decide to bolt if and when they signed Manning).

NOT A TERRIBLE GROUP OF QBs, by the way.

That was back when Harbaugh was being ultra-effusive about Smith, but after the NFC title-game loss and Manning became available, Harbaugh really never blinked in the chase for Manning.

And now, the 49ers are going on after recently losing an NFC title game and Harbaugh is being ultra-effusive about Kaepernick, so…

Wait. I’m not suggesting the 49ers will make a move for somebody to challenge Kaepernick’s starting spot in 2014. Not at all.

Harbaugh put a lot of credibility on the line in 2012 when made the switch from Smith to Kaepernick, he has mostly been proven right, and the 49ers have a young, dynamic QB who has been paid very little the last two years–a huge part of their playoff runs the past two seasons.

But after that wrenching loss to Seattle in the NFC Championship Game, I just think it’s wise to remember that Harbaugh, Baalke and York have a history of going through every off-season option.

There won’t be another Peyton-level QB available for nothing–that was a once-in-a-generation possibility, and we see how it turned out for the team that got Manning.

One thing we’ve learned about the Harbaugh-Baalke-York triumvirate is that they often drop into situations–in the chase for a Super Bowl–you wouldn’t have normally expected.

Such as…

Back in March 2012, Manning was an unrestricted free agent but was clearly looking to stay in the AFC all along, and he bonded with Broncos exec John Elway, which is why he picked Denver…

Let’s go through each side of this one, with two years of hindsight, and try to figure out what it all means now…

* PEYTON MANNING made the right call, obviously. He got to stay in the AFC, he landed with a franchise uniquely set up to his abilities and personality, and he just threw 55 TD passes to set a new NFL record.

What would’ve happened if he’d signed with the 49ers? Impossible to know, and I don’t like to guess at these things–you can’t know if he would’ve stayed healthy, if he would’ve flourished in the Harbaugh/Roman offense, if he would’ve had chemistry with the 49ers receivers.

He would’ve been good, though. We know that. And he’s one victory away from his second Super Bowl title. There will be a lot of talk about his legacy if he wins–and I might be doing some of it–but most of Manning’s legacy is set.

With this last burst in the past two seasons because of his decision to go to Denver, Manning has unquestionably moved into the ranks as one of the top five NFL QBs of all time.

* THE 49ERS were not wrong to chase Manning; again, it’s impossible to know how much things would’ve been different last season (when the 49ers were one play away from winning the Super Bowl with Kaepernick taking over from Smith at mid-season) or this season (when the 49ers were one play away from beating Seattle in the NFC Championship Game)…

At the time they were trying to sign Manning, the 49ers knew they had Kaepernick developing–they probably assumed Kaepernick was one or two seasons away from becoming a winning NFL QB; it turns out, he was only a half-season away from taking over the 49ers offense.

Harbaugh and Baalke weren’t sure, until Smith’s injury and Kaepernick’s play made them sure, and it isn’t wrong to try to pile up all the QB talent possible.

The attempt to sign Manning so soon after Smith guided the 49ers to the NFC title game, however, showed that Harbaugh wasn’t as sold on Smith as he always said he was. Again, that wasn’t wrong, but it was insight into the way Harbaugh and the 49ers work.

* ALEX SMITH made the right call to stick it out with the 49ers for one more season, even after he had to watch the 49ers go after Manning and even knowing Kaepernick was on the horizon.

He played very well before he got hurt in 2012, experienced the Kaepernick ascension, then Smith was traded after the 2012 season to Kansas City for two 2nd-round draft picks.

He’s better off for having gone through all that he went through with the 49ers, and he’s better off in KC now with Andy Reid and a franchise set up around his skill set.

I guess the 49ers could’ve kept Smith as Kaepernick’s back up this season, but that wouldn’t have worked out well in the locker room–Smith deserves to be an NFL starter, and if it couldn’t be with the 49ers, it had to be elsewhere, and Smith’s 2013 season in KC proved that.

* KAEPERNICK is the QB the 49ers ended up with, probably for the long-, long-term, and that’s a good thing.

After his explosive debut season in 2012, this season Kaepernick started all 16 games, the 49ers went 12-4, and his runs and throws were huge factors in the 49ers’ road playoff victories over Green Bay and Carolina.

Harbaugh wanted to get more dynamic at the QB position, so, even after all the work to build Alex Smith back up, he had his eye on Kaepernick the whole time–drafting him in 2011, developing him, developing him…

I’ve written many times that I thought the chase for Manning had a little Kaepernick Component, too–what better QB for Kaepernick to study under for a year or two than Peyton?

They are essentially opposites right now:

-Manning is limited physically and doesn’t throw tightest spirals, but he reads, he anticipates, he gets the ball out exactly when he needs to and where he needs to;

-Kaepernick is instinctive, incredibly athletic, and sometimes doesn’t quite read things correctly and force passes where they shouldn’t go, as we all saw again in Seattle a few Sundays ago.

But the 49ers are in a good spot with Kaepernick, who, of course, is still only 26 and has started only 29 regular- and postseason games and has already won more big games on the road than most QBs do in their whole careers.

Can Kaepernick win a Super Bowl? He almost won one two years ago and he was close enough this season, again, at a very young point in his career, to figure that yes, with the right circumstances he can win one or two down the road.

By the way, I’ve seen some 49ers fans arguing that Smith would’ve gotten them past Seattle and I can only respond: That’s being incredibly situational–maybe Smith doesn’t make those two bad INT throws in the fourth quarter, but do you think he makes those runs in the first half to get the 49ers ahead?

Do you think Smith makes the plays down the stretch in Green Bay? Throws those passes to Anquan Boldin in key moments throughout the season? Impossible to know for sure, but Kaepernick did make those plays, and I’m sure there’s little regret in 49ers HQ about that decision.

And now we’ll see what happens in the negotiations between the 49ers and Kaepernick for a long-term deal…

But as this all flows, maybe Kaepernick can learn a lesson about the Manning pursuit two years ago: The 49ers will be searching to get better, to make that leap to Lombardi Trophy Land, and if they think they can upgrade any position–even QB–they’ll take a shot at it.

Plus, I believe the 49ers will draft a QB with one of their many picks… not as direct competition for Kaepernick, but just to have somebody they can groom and maybe count on if Kaepernick gets hurt… who is not Colt McCoy.

It’s the way the 49ers do business, especially at the QB position. It’s not about sentiment or satisfaction. It’s about chasing the Super Bowl.

* Epilogue: Remember, AFTER the Peyton drama in 2012, the 49ers even reportedly thought about trading Kaepernick for a 2nd-round pickduring the 2012 draft but that, according to ESPN’s Adam Schefter, was nixed when the Eagles refused to give up the pick because they thought they could land Russell Wilson in a later round.

Turns out Seattle grabbed Wilson with a higher 3rd-rounder (75th overall)… and Philly had to settle for Nick Foles with the 88th pick.

That didn’t wind up too bad for any of these teams, eh? (Except the ones that didn’t take Wilson or Foles or have Kaepernick.)